I have a K&N filter with I believe a AFM intake. I run the TST power max and a quadzilla commander. The commander will automatically defuel the engine at pre determined settings there is no harm done to the engine. For example my EGT alert is set at 1300 and the commander will automatically defuel the engine at 1325. You can set alerts for EGT BOOST, FUEL PRESSURE, and others up to 7 parameters. I would highly reccomend the commander for monitor/safeguard for your box modded diesel.
My brother n law runs banks stage 3 kit on his 2000 7.3 and loves it the only thing he complained about is the $$$$ it cost him.
Hope it helps some